Stopes attended University College London as a scholarship student studying botany and geology, graduating with a first class B.Sc. in 1902. After carrying out research at University College London she pursued further study at the University of Munich, receiving a Ph.D. in palaeobotany in 1904. Following this Stopes earned a D.Sc. degree from University College London, becoming the youngest person in Britain to have done so. In 1903 she published a study of the botany of the recently dried-up Ebbsfleet River. In 1907 she went to Japan on a scientific mission, spending a year and a half at the Imperial University, Tokyo, exploring for fossil plants. She was also Fellow and sometime Lecturer in Palaeobotany at University College London and Lecturer in Palaeobotany at the University of Manchester (she held the post at Manchester from 1904 to 1907; in this capacity she became the first female academic of the University of Manchester).

During Stopes's time at Manchester, she studied coal and the collection of Glossopteris (seed ferns). This was an attempt to prove the theory of Eduard Suess concerning the existence of Gondwanaland or Pangaea. A chance meeting with Robert Falcon Scott (Scott of the Antarctic) during one of his fund-raising lectures brought a possibility of proving Suess's theory. Stopes's passion to prove Suess's theory led her to discuss with Scott the possibility of joining his next expedition. She failed to join the expedition but Scott had promised to bring back samples of fossils to prove the theory of the existence of Gondwanaland. A little more information can be found at the Geological Society web site concerning this area Cold Comfort.

Stopes opened the UK's first family planning clinic, the Mothers' Clinic at 61, Marlborough Road, Holloway, North London on 17 March 1921.

In 1925 the Mothers' Clinic moved to Central London, where it remains to this day.

Stopes and her fellow family planning pioneers around the globe, like Dora Russell, played a major role in breaking down taboos about sex and increasing knowledge, pleasure and improved reproductive health. In 1930 the National Birth Control Council was formed.

Stopes was a prominent campaigner for the implementation of policies inspired by eugenics, then not a discredited science. In her Radiant Motherhood (1920) she called for the "sterilisation of those totally unfit for parenthood [to] be made an immediate possibility, indeed made compulsory."

She contributed a chapter manifesto to The Control of Parenthood (1920), comprising a sort of manifesto for her circle of Eugenicists, arguing for a "utopia" to be achieved through "racial purification":

Those who are grown up in the present active generations, the matured and hardened, with all their weaknesses and flaws, cannot do very much, though they may do something with themselves. They can, however, study the conditions under which they came into being, discover where lie the chief sources of defect, and eliminate those sources of defect from the coming generation so as to remove from those who are still to be born the needless burdens the race has carried.

However, in this tract, she argues that the leading causes of "racial degeneration" are "overcrowding" and sexually transmitted disease (ibid, p. 211). It concludes somewhat vaguely, that racial consciousness needs to be increased so that, "women of all classes [may] have the fear and dread of undesired maternity removed from them ..." to usher in the promised utopia, described throughout. (ibid, p. 221)

She also bemoaned the abolition of child labour for the lower classes:

"Crushed by the burden of taxation which they have not the resources to meet and to provide for children also: crushed by the national cost of the too numerous children of those who do not contribute to the public funds by taxation, yet who recklessly bring forth from an inferior stock individuals who are not self-supporting, the middle and superior artisan classes have, without perceiving it, come almost to take the position of that ancient slave population."

In 1935 Stopes attended the International Congress for Population Science in Berlin, held under the Nazi regime. She was more than once accused of being anti-Semitic by other pioneers of the birth control movement such as Havelock Ellis.

As came to public attention years later, she was a personal as well as political devotee of Adolf Hitler:

“Dear Herr Hitler, Love is the greatest thing in the world: so will you accept from me these (poems) that you may allow the young people of your nation to have them?” These gushing words from an ardent fan (she was lucky Unity Mitford did not scratch her eyes out) were written in August 1939, just a month before this country went to war with Nazi Germany, by Marie Stopes [...]

After her son Harry married a myopic woman, Stopes cut him out of her will. The daughter-in-law—Mary Eyre Wallis, later Mary Stopes-Roe—was the daughter of the noted engineer Barnes Wallis. Stopes reasoned that prospective grandchildren might inherit the condition.

Supporters of Stopes generally concede that she made such remarks, but argue that they should be read in their historical context.

Following the death of Marie Stopes in 1958, a large part of her personal fortune went to the Eugenics Society.

Marie Carmichael Stopes was the daughter of Henry Stopes and Charlotte Carmichael Stopes.

Prior to her claim that her marriage to Canadian geneticist Reginald Ruggles Gates in 1911 was unconsummated, she had a serious relationship with Japanese botanist Kenjiro Fujii or Fugii, whom she met at the University of Munich in 1904 whilst researching her Ph.D. It was so serious, that in 1907, during her 1904-1910 tenure at Manchester University, she went to be with him in Japan, but the affair ended. Her marriage to Gates was annulled in 1914.

In 1918 she married the financial backer of her most famous work, Married Love: A New Contribution to the Solution of the Sex Difficulties, Humphrey Verdon Roe, brother of Alliott Verdon Roe. Their son, the philosopher Harry Stopes-Roe, was born in 1924.

Stopes died at her home in Dorking, Surrey, UK from breast cancer.

From the 1920s onward, Marie Stopes gradually built up a small network of clinics that were initially very successful, but by the early 1970s were in financial difficulties. In 1975 the clinics went into voluntary receivership. The modern organisation that bears Marie Stopes' name was established a year later as an international Non-Governmental Organisation working on Sexual and Reproductive Health. The Marie Stopes International (MSI) global partnership took over responsibility for the main clinic, and in 1978 it began its work overseas in New Delhi. Since then the organisation has grown steadily and today the MSI works in 38 countries, has 452 clinics worldwide and has offices in London, Brussels, Melbourne and USA.

In 2006 alone, the organisation provided services to 4.6 million clients and by 2010 aims to protect 20 million couples from unplanned pregnancies and unsafe abortion.

Marie Stopes founded Portland Museum, Dorset on the Isle of Portland, which opened in 1930, and acted as the museum's curator. The cottage housing the museum was an inspiration behind The Well-Beloved, a novel by Thomas Hardy, who was a friend of Marie Stopes.